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. 2022 Jul 8:13:883446.
doi: 10.3389/fimmu.2022.883446. eCollection 2022.

Targeted Gene Sanger Sequencing Should Remain the First-Tier Genetic Test for Children Suspected to Have the Five Common X-Linked Inborn Errors of Immunity

Koon-Wing Chan  1 , Chung-Yin Wong  1 , Daniel Leung  1 , Xingtian Yang  1 , Susanna F S Fok  1 , Priscilla H S Mak  1 , Lei Yao  1 , Wen Ma  1 , Huawei Mao  2 , Xiaodong Zhao  3 , Weiling Liang  4 , Surjit Singh  5 , Mohamed-Ridha Barbouche  6 , Jian-Xin He  7 , Li-Ping Jiang  3 , Woei-Kang Liew  8 , Minh Huong Thi Le  9 , Dina Muktiarti  10 , Fatima Johanna Santos-Ocampo  11 , Reda Djidjik  12 , Brahim Belaid  12 , Intan Hakimah Ismail  13 , Amir Hamzah Abdul Latiff  14 , Way Seah Lee  15 , Tong-Xin Chen  16 , Jinrong Liu  7 , Runming Jin  17 , Xiaochuan Wang  18 , Yin Hsiu Chien  19 , Hsin-Hui Yu  20 , Dinesh Raj  21 , Revathi Raj  22 , Jenifer Vaughan  23 , Michael Urban  24 , Sylvia van den Berg  25 , Brian Eley  26 , Anselm Chi-Wai Lee  27 , Mas Suhaila Isa  28 , Elizabeth Y Ang  28 , Bee Wah Lee  28   29 , Allen Eng Juh Yeoh  28   29 , Lynette P Shek  29   30 , Nguyen Ngoc Quynh Le  31 , Van Anh Thi Nguyen  32 , Anh Phan Nguyen Lien  33 , Regina D Capulong  34 , Joanne Michelle Mallillin  35 , Jose Carlo Miguel M Villanueva  36 , Karol Anne B Camonayan  37 , Michelle De Vera  38 , Roxanne J Casis-Hao  39 , Rommel Crisenio M Lobo  40 , Ruby Foronda  41 , Vicky Wee Eng Binas  42 , Soraya Boushaki  12   43 , Nadia Kechout  44 , Gun Phongsamart  45 , Siriporn Wongwaree  45 , Chamnanrua Jiratchaya  45 , Mongkol Lao-Araya  46 , Muthita Trakultivakorn  46 , Narissara Suratannon  47 , Orathai Jirapongsananuruk  48 , Teerapol Chantveerawong  49 , Wasu Kamchaisatian  50 , Lee Lee Chan  51 , Mia Tuang Koh  15 , Ke Juin Wong  52 , Siew Moy Fong  52 , Meow-Keong Thong  53 , Zarina Abdul Latiff  54 , Lokman Mohd Noh  54   55 , Rajiva de Silva  56 , Zineb Jouhadi  57 , Khulood Al-Saad  58 , Pandiarajan Vignesh  5 , Ankur Kumar Jindal  5 , Amit Rawat  5 , Anju Gupta  5 , Deepti Suri  5 , Jing Yang  1 , Elaine Yuen-Ling Au  59 , Janette Siu-Yin Kwok  60 , Siu-Yuen Chan  1 , Wayland Yuk-Fun Hui  1 , Gilbert T Chua  1 , Jaime Rosa Duque  1 , Kai-Ning Cheong  61 , Patrick Chun Yin Chong  62 , Marco Hok Kung Ho  62 , Tsz-Leung Lee  61 , Wilfred Hing-Sang Wong  1 , Wanling Yang  1 , Pamela P Lee  1 , Wenwei Tu  1 , Xi-Qiang Yang  3 , Yu Lung Lau  1
Affiliations

Targeted Gene Sanger Sequencing Should Remain the First-Tier Genetic Test for Children Suspected to Have the Five Common X-Linked Inborn Errors of Immunity

Koon-Wing Chan et al. Front Immunol. .

Abstract

To address inborn errors of immunity (IEI) which were underdiagnosed in resource-limited regions, our centre developed and offered free genetic testing for the most common IEI by Sanger sequencing (SS) since 2001. With the establishment of The Asian Primary Immunodeficiency (APID) Network in 2009, the awareness and definitive diagnosis of IEI were further improved with collaboration among centres caring for IEI patients from East and Southeast Asia. We also started to use whole exome sequencing (WES) for undiagnosed cases and further extended our collaboration with centres from South Asia and Africa. With the increased use of Next Generation Sequencing (NGS), we have shifted our diagnostic practice from SS to WES. However, SS was still one of the key diagnostic tools for IEI for the past two decades. Our centre has performed 2,024 IEI SS genetic tests, with in-house protocol designed specifically for 84 genes, in 1,376 patients with 744 identified to have disease-causing mutations (54.1%). The high diagnostic rate after just one round of targeted gene SS for each of the 5 common IEI (X-linked agammaglobulinemia (XLA) 77.4%, Wiskott-Aldrich syndrome (WAS) 69.2%, X-linked chronic granulomatous disease (XCGD) 59.5%, X-linked severe combined immunodeficiency (XSCID) 51.1%, and X-linked hyper-IgM syndrome (HIGM1) 58.1%) demonstrated targeted gene SS should remain the first-tier genetic test for the 5 common X-linked IEI.

Keywords: Sanger sequencing; inborn errors of immunity; next generation sequencing; primary immunodeficiency diseases; targeted gene; whole exome sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Map showing 72 referring centres in 17 countries. (Created with Datawrapper).
Figure 2
Figure 2
Number of patients with first round of targeted gene SS (Sanger Sequencing) performed, and number of patients with mutations identified. IEI, inborn errors of immunity; SS, Sanger sequencing; BTK, Bruton tyrosine kinase; WAS, WASP actin nucleation promoting factor; CYBB, cytochrome b-245 beta chain; IL2RG, interleukin 2 receptor subunit gamma; CD40LG; CD40 ligand.
Figure 3
Figure 3
Number of patients with targeted gene SS performed, and number of patients with mutations identified. Official gene symbols approved by HGNC were used. Approved full gene names are available in HGNC. IEI, inborn errors of immunity; SS, Sanger sequencing; HGNC; HUGO Gene Nomenclature Committee.
Figure 4
Figure 4
Distribution of casual mutations in various exons, exon-intron junctions and corresponding domains of BTK gene. The upper diagram shows the distribution and frequency of amino acid mutations in various protein domains; while the lower diagram shows the locations of splice site mutations and large deletions of the gene. BTK, Bruton tyrosine kinase; XLA, X-linked agammaglobulinemia; PH, Pleckstrin homology; SH2, Src homology 2; SH3. Src homology 3.
Figure 5
Figure 5
Distribution of casual mutations in various exons, exon-intron junctions and corresponding domains of WAS gene. The upper diagram shows the distribution and frequency of amino acid mutations in various protein domains; while the lower diagram shows the locations of splice site mutations and large deletions of the gene. WAS, WASP actin nucleation promoting factor; WAS, Wiskott Aldrich Syndrome; PBD, P21-Rho-binding domain; WH1, WASP homology 1 domain; WH2, WASP homology 2 domain.
Figure 6
Figure 6
Distribution of casual mutations in various exons, exon-intron junctions and corresponding domains of CYBB gene. The upper diagram shows the distribution and frequency of amino acid mutations in various protein domains; while the lower diagram shows the locations of splice site mutations and large deletions of the gene. CYBB, cytochrome b-245 beta chain; XCGD, X-linked chronic granulomatous disease.
Figure 7
Figure 7
Distribution of casual mutations in various exons, exon-intron junctions and corresponding domains of IL2RG gene. The upper diagram shows the distribution and frequency of amino acid mutations in various protein domains; while the lower diagram shows the locations of splice site mutations and large deletions of the gene. IL2RG, interleukin 2 receptor subunit gamma; XSCID, X-linked severe combined immunodeficiency.
Figure 8
Figure 8
Distribution of casual mutations in various exons, exon-intron junctions and corresponding domains of IL2RG gene. The upper diagram shows the distribution and frequency of amino acid mutations in various protein domains; while the lower diagram shows the locations of splice site mutations and large deletions of the gene. CD40LG; CD40 ligand; HIGM1, X-linked immunodeficiency with hyper-IgM type 1.
See this image and copyright information in PMC

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